SMTL ID : 6p8b.1

E.coli LpxD in complex with peptide FITC-RJPXD33

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-3-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.2: 3 residues within 4Å: Chain A: N.123 Chain B: N.123 Chain C: N.123 No protein-ligand interaction detected (PLIP)

2 x O3V: 3-hydroxy-7,7-dimethyl-2-phenyl-4-(thiophen-2-yl)-2,6,7,8-tetrahydro-5H-pyrazolo[3,4-b]quinolin-5-one(Non-covalent)

O3V.3: 20 residues within 4Å: Chain A: F.185, Y.187, W.194, I.256, M.257, A.258, V.274, I.275, N.276 Chain B: I.232, A.250, A.252, G.253, M.268, I.269, G.270, G.271, T.286, V.287, T.288 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:I.232, B:A.250, B:A.252, A:F.185, A:F.185, A:Y.187, A:W.194, A:I.256, A:A.258 Hydrogen bonds: B:G.271 O3V.4: 20 residues within 4Å: Chain B: F.185, Y.187, W.194, Q.238, I.256, A.258, V.274, N.276 Chain C: I.232, D.234, A.250, A.252, G.253, M.268, I.269, G.270, G.271, T.286, V.287, T.288 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.185, B:F.185, B:I.256, B:A.258, C:I.232, C:A.252 Hydrogen bonds: C:G.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, X. et al., Structural and Biological Basis of Small Molecule Inhibition ofEscherichia coliLpxD Acyltransferase Essential for Lipopolysaccharide Biosynthesis. Acs Infect Dis. (2020)

Release Date

2019-08-28

Peptides

UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase: ABC
FITC-RJPXD33: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
L

UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase

FITC-RJPXD33

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